Prion diseases are neurodegenerative disorders of humans and animals that involve misfolding of prion protein (PrP). These diseases can present as genetic, infectious or sporadic illnesses and each type is often transmissible to experimental animals. Diseases caused by prions include scrapie, bovine spongiform encephalopathy (BSE), and Creutzfeldt-Jakob disease (CJD) in humans. All prion diseases involve changes in the conformation of PrP from its benign cellular isoform, PrPC, to a disease-specific isoform, PrPsc. PrPsc is probably the sole functional component of the infectious particle and different conformations of PrPsc can encipher properties of prion strains. Originally thought to be diseases caused by an exogenous slow virus, convincing evidence now indicates that prion diseases are disorders of protein conformation. The discovery of a new principle of infection resulted from research involving many disciplines focused on PrP. The four senior investigators on this Program Project application propose to extend their collaborative prion research efforts in a new direction. Although PrP is central to infectivity, disease susceptibility and pathogenesis, other molecules also are involved. Recent discoveries provide the first opportunity to study mechanisms of prion replication and pathogenesis by focusing on genes other than that encoding PrP. Treating scrapie incubation time as a quantitative trait allowed the identification chromosomal regions harboring prion incubation time modifier genes. These genes will be identified using positional cloning and positional candidate approaches, aided by new technologies in DNA analysis, expression microarrays and BAC engineering for production of transgenic mice. Additional prion modifier genes will be identified by sampling natural polymorphisms in mouse strains using QTL analysis and by applying chemical mutagenesis to screen for novel prion incubation time genes. The first gene encoding a PrP-related protein, Dpl, was discovered downstream from the PrP gene. Although PrP and DpI exhibit only 25% sequence identity, they share a conserved three-helix bundle structure. This provides a unique opportunity to learn more about prion replication and disease pathogenesis through creation of chimeric PrP:Dpl molecules. DpI misexpression in brain causes cerebellar neurodegeneration that can be prevented by PrP expression, suggesting involvement of similar pathways which will be interrogated with cDNA arrays and by identification of modifier genes. In addition to providing a new perspective on prion disease, these studies may ultimately reveal pathways common to a variety of CNS degenerative disorders.